vene
commented
13 years ago I would like to add that I also get some segmentation faults when testing with 64-bit OS X 10.7, specifically everything from the manifold learning module crashes. Is there a "correct" way to build scikit-learn on this platform?
I have the previous scipy superpack installed; I couldn't for the life of me build scipy without its tests hanging.
Vlad
On Wed, Nov 9, 2011 at 2:51 AM, Dawen Liang reply@reply.github.com wrote:
Hi all,
Thanks to the help this afternoon, I finally got sklearn working with my test logistic regression. However, while I run the test, I got the segmentation fault at last, here is the output (very long), it seems to me that something is not implemented yet and not sure if that's the cause of the error:
Running unit tests and doctests for sklearn NumPy version 2.0.0.dev-7297785 NumPy is installed in /Library/Python/2.7/site-packages/numpy-2.0.0.dev_7297785_20111104-py2.7-macosx-10.7-x86_64.egg/numpy Python version 2.7.1 (r271:86832, Jun 16 2011, 16:59:05) [GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)] nose version 1.1.2 /Library/Python/2.7/site-packages/scikit_learn-0.10_git-py2.7-macosx-10.7-intel.egg/sklearn/cross_val.py:2: UserWarning: sklearn.cross_val namespace is deprecated in version 0.9 and will be removed in version 0.11. Please use sklearn.cross_validation instead. warnings.warn('sklearn.cross_val namespace is deprecated in version 0.9' /Library/Python/2.7/site-packages/scikit_learn-0.10_git-py2.7-macosx-10.7-intel.egg/sklearn/hmm.py:16: UserWarning: sklearn.hmm is orphaned, undocumented and has known numerical stability issues. If nobody volunteers to write documentation and make it more stable, this module will be removed in version 0.11. warnings.warn('sklearn.hmm is orphaned, undocumented and has known numerical' .........../Library/Python/2.7/site-packages/scikit_learn-0.10_git-py2.7-macosx-10.7-intel.egg/sklearn/neighbors/base.py:23: UserWarning: kneighbors: neighbor k+1 and neighbor k have the same distance: results will be dependent on data order. warnings.warn(msg) ......../Library/Python/2.7/site-packages/scikit_learn-0.10_git-py2.7-macosx-10.7-intel.egg/sklearn/cluster/kmeans.py:219: UserWarning: Explicit initial center position passed: performing only one init in the k-means warnings.warn('Explicit initial center position passed: ' .............../Library/Python/2.7/site-packages/scikit_learn-0.10_git-py2.7-macosx-10.7-intel.egg/sklearn/cluster/spectral.py:77: UserWarning: pyamg not available, using scipy.sparse warnings.warn('pyamg not available, using scipy.sparse') .S...................S.S.........................FFF............/Library/Python/2.7/site-packages/scikit_learn-0.10git-py2.7-macosx-10.7-intel.egg/sklearn/decomposition/fastica.py:199: UserWarning: Please note: the interface of fastica has changed: X is now assumed to be of shape [n_samples, n_features] warnings.warn("Please note: the interface of fastica has changed: " ..................../Library/Python/2.7/site-packages/scikit_learn-0.10_git-py2.7-macosx-10.7-intel.egg/sklearn/decomposition/nmf.py:237: UserWarning: Iteration limit reached in nls subproblem. warnings.warn("Iteration limit reached in nls subproblem.") .................../Library/Python/2.7/site-packages/scikit_learn-0.10_git-py2.7-macosx-10.7-intel.egg/sklearn/decomposition/sparse_pca.py:146: RuntimeWarning: invalid value encountered in divide U /= np.sqrt((U \ 2).sum(axis=0)) ......................./Library/Python/2.7/site-packages/scikit_learn-0.10_git-py2.7-macosx-10.7-intel.egg/sklearn/externals/joblib/test/test_func_inspect.py:101: UserWarning: Cannot inspect object <functools.partial object at 0x103a760a8>, ignore list will not work. nose.tools.assert_equal(filter_args(ff, ['y'], 1), ........................................................................................____ test_memory setup
test_memory teardown
..____ test_memory setup
......................................................................................................................____ test_memory teardown
.____ setup numpy_pickle
.......................................Failed to save <class 'numpy.ma.core.MaskedArray'> to .npy file: Traceback (most recent call last): File "/Library/Python/2.7/site-packages/scikit_learn-0.10_git-py2.7-macosx-10.7-intel.egg/sklearn/externals/joblib/numpy_pickle.py", line 62, in save self.np.save(filename, obj) File "/Library/Python/2.7/site-packages/numpy-2.0.0.dev_7297785_20111104-py2.7-macosx-10.7-x86_64.egg/numpy/lib/npyio.py", line 434, in save format.write_array(fid, arr) File "/Library/Python/2.7/site-packages/numpy-2.0.0.dev_7297785_20111104-py2.7-macosx-10.7-x86_64.egg/numpy/lib/format.py", line 409, in write_array array.tofile(fp) File "/Library/Python/2.7/site-packages/numpy-2.0.0.dev_7297785_20111104-py2.7-macosx-10.7-x86_64.egg/numpy/ma/core.py", line 5380, in tofile raise NotImplementedError("Not implemented yet, sorry...") NotImplementedError: Not implemented yet, sorry...
.____ teardown numpy_pickle
...............E..................................F................/Library/Python/2.7/site-packages/scikit_learn-0.10_git-py2.7-macosx-10.7-intel.egg/sklearn/linear_model/least_angle.py:218: RuntimeWarning: invalid value encountered in divide z = -coefs[n_iter, active] / least_squares ....Segmentation fault: 11
Any help will be appreciated. Thanks!
Reply to this email directly or view it on GitHub: https://github.com/scikit-learn/scikit-learn/issues/435
GaelVaroquaux
dawenl
pprett
Hi all,
Thanks to the help this afternoon, I finally got sklearn working with my test logistic regression. However, while I run the test, I got the segmentation fault at last, here is the output (very long), it seems to me that something is not implemented yet and not sure if that's the cause of the error:
Any help will be appreciated. Thanks!